IMPORTANT WARNING: Alignment column 40 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 101 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 102 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 103 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 199 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 204 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 205 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 206 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 218 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 219 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 469 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 624 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 676 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 677 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 690 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 854 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1413 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1457 contains only undetermined values which will be treated as missing data IMPORTANT WARNING Found 18 columns that contain only undetermined values which will be treated as missing data. Normally these columns should be excluded from the analysis. Just in case you might need it, an alignment file with undetermined columns removed is printed to file /auto/dufayard/res/ori_nucl_raxml/nucleic_M2845_68x1715_2006.phy.reduced You are using RAxML version 7.0.4 released by Alexandros Stamatakis in April 2008 Alignment has 649 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 0.047050 RAxML rapid hill-climbing mode Executing 1 inference on the original alignment using a distinct randomized MP tree All free model parameters will be estimated by RAxML GAMMA model of rate heteorgeneity, ML estimate of alpha-parameter GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units Partition: 0 Name: No Name Provided DataType: DNA Substitution Matrix: GTR Empirical Base Frequencies: pi(A): 0.250768 pi(C): 0.214082 pi(G): 0.276421 pi(T): 0.258728 1.435466 -11485.709593 3.356507 -11467.301602 8.990684 -11407.546286 17.122896 -11388.340530 26.728577 -11385.747629 36.257177 -11384.785797 45.322868 -11384.571805 54.269348 -11384.477198 65.814894 -11384.386696 75.913454 -11384.298712 86.537745 -11384.214249 94.151331 -11384.214249 102.937512 -11358.415231 Overall Time for 1 Inference 102.953344 Likelihood : -11358.415231 Parsimony starting tree written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_parsimonyTree.nucleic_M2845_68x1715_2006.phy_RAXML Final tree written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_result.nucleic_M2845_68x1715_2006.phy_RAXML Execution Log File written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_log.nucleic_M2845_68x1715_2006.phy_RAXML Execution information file written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_info.nucleic_M2845_68x1715_2006.phy_RAXML